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Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance.

ABSTRACT: Strophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNA-seq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed with salt. S. helvola plants were grown in pots and treated with half lethal-guided dose of NaCl solution for 3?h, 24?h, and 7d. The plants supplied with the same amount of water were used as controls. The whole roots sampled from the three time points were equally pooled as one biological replicate, and three replicates were used for library construction and transcriptome sequencing on Illumina Hiseq 2500. The comparative analyses of root transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in salt tolerance in S. helvola.

SUBMITTER: Zhang H

PROVIDER: S-EPMC6289113 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance.

Zhang Hengyou H Zuelsdorf Christine C Penneys Darin D Fan Shoujin S Kofsky Janice J Song Bao-Hua BH

Scientific data 20181211

Strophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNA-seq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed ...[more]

PMID: 30531857

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Project description:BACKGROUND:Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique. RESULTS:A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL, OsNAAT, OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29. CONCLUSIONS:The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k+, ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent.

Project description:Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, "Wnt signaling pathway" was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

Dataset Information

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance.

Publications

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance.

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